rs6950765

Variant names:

• chr7-117281176-C-G
• rs6950765
• NM_003391.3:c.854-2792G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003391.3(WNT2):​c.854-2792G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,030 control chromosomes in the GnomAD database, including 31,207 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.64 (31207 hom., cov: 31)
• Consequence: WNT2 NM_003391.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 6 publications found

Genes affected

WNT2 (HGNC:12780): (Wnt family member 2) This gene is a member of the WNT gene family. The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WNT2	NM_003391.3	c.854-2792G>C		intron_variant	Intron 4 of 4	ENST00000265441.8	NP_003382.1
WNT2	NR_024047.2	n.859-2792G>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WNT2	ENST00000265441.8	c.854-2792G>C		intron_variant	Intron 4 of 4	1	NM_003391.3	ENSP00000265441.3
WNT2	ENST00000449446.5	n.*457-2792G>C		intron_variant	Intron 4 of 4	3		ENSP00000389643.1
WNT2	ENST00000647844.1	n.*769-2792G>C		intron_variant	Intron 5 of 5			ENSP00000497695.1

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97017 AN: 151912 Hom.: 31174 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.649

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.639 AC: 97093 AN: 152030 Hom.: 31207 Cov.: 31 AF XY: 0.643 AC XY: 47785 AN XY: 74300

African (AFR) AF: 0.689 AC: 28601 AN: 41488

American (AMR) AF: 0.673 AC: 10292 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2057 AN: 3472

East Asian (EAS) AF: 0.742 AC: 3828 AN: 5156

South Asian (SAS) AF: 0.661 AC: 3185 AN: 4816

European-Finnish (FIN) AF: 0.615 AC: 6486 AN: 10544

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40551 AN: 67956

Other (OTH) AF: 0.643 AC: 1355 AN: 2108

Alfa AF: 0.621 Hom.: 3644

Bravo AF: 0.647

Asia WGS AF: 0.723 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.40
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6950765; hg19: chr7-116921230;